#!/usr/bin/env python
# coding: utf-8

# ## Coupled pair of reactions: `A <-> B` , and  `A + E <-> B + E`
# A direct reaction and the same reaction, catalyzed
# ### Enzyme `E` initially zero, and then suddenly added mid-reaction
# 
# LAST REVISED: June 23, 2024 (using v. 1.0 beta36)

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import set_path      # Importing this module will add the project's home directory to sys.path


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from life123 import ChemData
from life123 import UniformCompartment


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# Initialize the system
chem_data = ChemData(names=["A", "B", "E"])

# Reaction A <-> B , with 1st-order kinetics, favorable thermodynamics in the forward direction, 
# and a forward rate that is much slower than it would be with the enzyme - as seen in the next reaction, below
chem_data.add_reaction(reactants="A", products="B",
                       forward_rate=1., delta_G=-3989.73)

# Reaction A + E <-> B + E , with 1st-order kinetics, and a forward rate that is faster than it was without the enzyme
# Thermodynamically, there's no change from the reaction without the enzyme
chem_data.add_reaction(reactants=["A", "E"], products=["B", "E"],
                       forward_rate=10., delta_G=-3989.73)

chem_data.describe_reactions()     # Notice how the enzyme `E` is noted in the printout below


# ### Set the initial concentrations of all the chemicals - starting with no enzyme

# In[4]:


dynamics = UniformCompartment(chem_data=chem_data, preset="mid")
dynamics.set_conc(conc={"A": 20.},
                  snapshot=True)      # Initially, no enzyme `E`
dynamics.describe_state()


# ### Advance the reactions (for now without enzyme), but stopping well before equilibrium

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dynamics.set_diagnostics()       # To save diagnostic information about the call to single_compartment_react()

# Perform the reactions
dynamics.single_compartment_react(duration=0.25,
                                  initial_step=0.05, variable_steps=True)


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#dynamics.explain_time_advance()


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dynamics.plot_history(colors=['darkorange', 'green', 'violet'], show_intervals=True, title_prefix="WITH zero enzyme")


# ### The reactions, lacking enzyme, are proceeding slowly towards equilibrium, just like the reaction that was discussed in part 1 of the experiment "enzyme_1"

# # Now suddently add a lot of enzyme

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dynamics.set_single_conc(30., species_name="E", snapshot=True)    # Plenty of enzyme `E`


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dynamics.describe_state()


# ### Take the system to equilibrium

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dynamics.single_compartment_react(duration=0.04,
                                  initial_step=0.005, variable_steps=True)


# #### Note how the (proposed) initial step - in spite of having been reduced from the earlier run - is now appearing _large_, given the much-faster reaction dynamics.  However, the variable-step engine intercepts and automatically corrects the problem!

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#dynamics.explain_time_advance()


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dynamics.plot_history(colors=['darkorange', 'green', 'violet'], show_intervals=True, title_prefix="WITH enzyme added mid-reaction")


# ## Notice the dramatic acceleration of the reaction as soon as the enzyme `E` is added at t = 0.275!
# The reactions simulator automatically switches to small time steps is in order to handle the rapid amount of change

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# Verify that the reaction has reached equilibrium
dynamics.is_in_equilibrium()


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dynamics.get_history()


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